Regulation of Directionality in Bacteriophage λ Site-specific Recombination: Structure of the Xis Protein

Sam, My D.; Papagiannis, Christie V.; Connolly, Kevin M.; Corselli, Leah; Iwahara, Junji; Lee, James; Phillips, Martin; Wojciak, Jonathan M.; Johnson, Reid C.; Clubb, Robert T.

doi:10.1016/s0022-2836(02)01150-6

Cited by 48 publications

(87 citation statements)

References 62 publications

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“…The model was constructed by manually docking the structures of 15 N INT-DBD (27) and Xis C28S (residues 1-55 of the excisionase protein with a cysteine-to-serine mutation at position 28; ref. 28) to B-form DNA by using the program MOLMOL (39).…”

Section: Nmr Studiesmentioning

confidence: 99%

“…Biochemical and genetic studies have suggested that the carboxyl-terminal tail of Xis directly contacts INT-DBD 1-64 because it is required for cooperative binding of Xis and INT-DBD 1-64 to sites P2 and X1 (29,30,41). In the absence of DNA, the carboxyl-terminal tail of Xis is unstructured and presumed to undergo a disorderedto-ordered transition in the INT-DBD 1-64 -Xis-DNA ternary complex (28). To test whether this tail directly contacts INT-DBD 1-64 , we performed a peptide titration study.…”

Section: E47 Plays a Role In Both Integrative And Excisive Recombinatmentioning

confidence: 99%

“…These include x-ray crystal structures of Fis protein (21)(22)(23), IHF bound to its cognate DNA site (24), the unliganded catalytic domain of (25), the DNA-liganded carboxyl-terminal domain of (26) and the NMR structures of the amino-terminal domains of Int (27) and Xis (28). As a step toward understanding how these structures fit and function together, we describe the interactions of the amino-terminal domain of Int with itself and with Xis.…”

mentioning

confidence: 99%

“…The first 50 residues of Xis adopt a winged-helix structure that is thought to be responsible for DNA binding at the X1 and X2 sites on attR (28). The carboxyl-terminal residues (52-72), which are disordered in the absence of DNA, are required for interaction with Int bound at the adjacent P2 site (28)(29)(30).…”

mentioning

confidence: 99%

“…The carboxyl-terminal residues (52-72), which are disordered in the absence of DNA, are required for interaction with Int bound at the adjacent P2 site (28)(29)(30). The amino-terminal domain of Int, consisting of a three-stranded ␤-sheet and an ␣-helix, is proposed to recognize its cognate DNA arm sites through the three-stranded ␤-sheet (27).…”

mentioning

confidence: 99%

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Identification of the λ integrase surface that interacts with Xis reveals a residue that is also critical for Int dimer formation

Warren

Sam²,

Manley³

et al. 2003

Proc. Natl. Acad. Sci. U.S.A.

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Lambda integrase (Int) is a heterobivalent DNA-binding protein that together with the accessory DNA-bending proteins IHF, Fis, and Xis, forms the higher-order protein-DNA complexes that execute integrative and excisive recombination at specific loci on the chromosomes of phage and its Escherichia coli host. The large carboxyl-terminal domain of Int is responsible for binding to core-type DNA sites and catalysis of DNA cleavage and ligation reactions. The small amino-terminal domain (residues 1-70), which specifies binding to arm-type DNA sites distant from the regions of strand exchange, consists of a three-stranded ␤-sheet, proposed to recognize the cognate DNA site, and an ␣-helix. We report here that a site on this ␣-helix is critical for both homomeric interactions between Int protomers and heteromeric interactions with Xis. The mutant E47A, which was identified by alanine-scanning mutagenesis, abolishes interactions between Int and Xis bound at adjacent binding sites and reduces interactions between Int protomers bound at adjacent arm-type sites. Concomitantly, this residue is essential for excisive recombination and contributes to the efficiency of the integrative reaction. NMR titration data with a peptide corresponding to Xis residues 57-69 strongly suggest that the carboxyl-terminal tail of Xis and the ␣-helix of the aminoterminal domain of Int comprise the primary interaction surface for these two proteins. The use of a common site on Int for both homotypic and heterotypic interactions fits well with the complex regulatory patterns associated with this site-specific recombination reaction.T he bacteriophage -encoded integrase (Int) belongs to a subgroup of the tyrosine recombinase family known as the heterobivalent recombinases (1, 2). These recombinases catalyze reactions that are distinguished from other pathways of sitespecific rearrangement and movement of DNA by their directionality. This feature is built on the ability of these recombinases to simultaneously bind and bridge two distinct and well separated DNA-binding sites (3-5). Int binds with high affinity to arm-type DNA sites by means of a small amino-terminal domain (residues 1-70) whereas it binds with lower affinity to core-type sites by means of a larger carboxyl-terminal domain (residues 75-356), which also executes DNA strand cleavage and ligation. Bridging between arm and core sites is facilitated by DNA bends induced by accessory proteins (IHF, Xis, and Fis) bound to DNA sites located between the arm-and core-type sequences (5-9). This ensemble of DNA-bending-and DNA-bridging-proteins forms the large recombinogenic complexes that confer directionality on the recombination reaction. In this article we show that formation of both the Int-Xis and Int-Int complexes, key elements in the structure and function of the higher-order recombinogenic structures, depends on a common site in the amino-terminal domain of Int.The Int recombinase catalyzes the integration and excision of viral DNA into and out of the chromosome of its Escherichia coli...

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Section: Nmr Studiesmentioning

confidence: 99%

Section: E47 Plays a Role In Both Integrative And Excisive Recombinatmentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

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Identification of the λ integrase surface that interacts with Xis reveals a residue that is also critical for Int dimer formation

Warren

Sam²,

Manley³

et al. 2003

Proc. Natl. Acad. Sci. U.S.A.

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Retraction: Site‐specific recombination of nitrogen‐fixation genes in cyanobacteria by XisF–XisH–XisI complex: Structures and models, William C. Hwang, James W. Golden, Jaime Pascual, Dong Xu, Anton Cheltsov, Adam Godzik

et al. 2018

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Nitrogen fixation is an important process that converts atmospheric gaseous nitrogen, a form plants cannot utilize, into ammonia that can be easily assimilated. Large serine recombinase XisF (fdxN element site-specific recombinase), together with controlling factors XisH and XisI, plays a critical role in the expression of nitrogen fixation genes of certain Anabaena and Nostoc species of cyanobacteria. All three proteins are required to excise the fdxN DNA element from the chromosome in differentiating heterocysts for the expression of nitrogen fixation related genes. We report the first crystal structures of XisH and XisI proteins, both adopting novel protein folds. Based on the analysis of their sequences and structures, we propose that XisH and XisI proteins function as endonucleases and recombination directionality factors (RDFs), respectively.

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Isolation of Xis Gen Fragment of λ Phage from Agarose Gel Using Magnetic Particles for Subsequent Enzymatic DNA Sequencing

et al. 2012

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Regulation of Directionality in Bacteriophage λ Site-specific Recombination: Structure of the Xis Protein

Cited by 48 publications

References 62 publications

Identification of the λ integrase surface that interacts with Xis reveals a residue that is also critical for Int dimer formation

Identification of the λ integrase surface that interacts with Xis reveals a residue that is also critical for Int dimer formation

Retraction: Site‐specific recombination of nitrogen‐fixation genes in cyanobacteria by XisF–XisH–XisI complex: Structures and models, William C. Hwang, James W. Golden, Jaime Pascual, Dong Xu, Anton Cheltsov, Adam Godzik

Isolation of Xis Gen Fragment of λ Phage from Agarose Gel Using Magnetic Particles for Subsequent Enzymatic DNA Sequencing

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